o Rŀgv @sdZddlmZddlmZddlmZddlmZddlmZddlmZeeeedZ z dd lm Z e e d <Wn e yBYnwd d Z d dZ ddZdddZdS)zI/O function wrappers for phylogenetic tree formats. This API follows the same semantics as Biopython's ``SeqIO`` and ``AlignIO``. )File)BaseTree)NewickIO)NeXMLIO)NexusIO) PhyloXMLIO)newicknexusphyloxmlnexml)CDAOIOcdaocksRt|}tt|d|fi|EdHWddS1s"wYdS)alParse a file iteratively, and yield each of the trees it contains. If a file only contains one tree, this still returns an iterable object that contains one element. Examples -------- >>> import Bio.Phylo >>> trees = Bio.Phylo.parse('PhyloXML/apaf.xml', 'phyloxml') >>> for tree in trees: ... print(tree.rooted) True parseN)r as_handlegetattrsupported_formats)fileformatkwargsfprA/var/www/html/myenv/lib/python3.10/site-packages/Bio/Phylo/_io.pyr$s ""rcKsbzt||fi|}t|}Wn tytddwz t|Wtdty0|YSw)zParse a file in the given format and return a single tree. Raises a ``ValueError`` if there are zero or multiple trees -- if this occurs, use ``parse`` instead to get the complete sequence of trees. z There are no trees in this file.Nz;There are multiple trees in this file; use parse() instead.)rnext StopIteration ValueError)rrrtree_gentreerrrread7s     rcKsft|tjtjfr |g}t|d}tt|d||fi|}Wd|S1s,wY|S)z6Write a sequence of trees to file in the given format.zw+writeN) isinstancerTreeCladerrrr)treesrrrrnrrrrJs rNcKs2|duri}t||fi|}t|||fi|S)z&Convert between two tree file formats.N)rr)in_file in_formatout_file out_format parse_argsrr"rrrconvertTsr))N)__doc__Bior Bio.Phylorrrrrrr ImportErrorrrrr)rrrrs,